Services

Introduction to BioCyc

The BioCyc collection of Pathway/Genome Databases (PGDBs)
provides a reference on the genomes and metabolic pathways of
thousands of sequenced organisms. BioCyc PGDBs are generated by
software that predict the metabolic pathways of completely sequenced
organisms, predict which genes code for missing enzymes in metabolic
pathways, and predict operons. BioCyc also integrates information
from other bioinformatics databases, such as protein feature and Gene
Ontology information from UniProt. The BioCyc website provides a
suite of software tools for database searching and visualization, for
omics data analysis, and for comparative genomics and comparative
pathway questions.

BioCyc databases (DBs) are
organized into tiers according to the amount of manual
updating they have received.

Publications: Articles about BioCyc databases and the Pathway Tools software

BioCyc data files may be downloaded to your site, and BioCyc
data can be queried via web services.
And you can install BioCyc on computers at your site,
running it as a local Web server, and/or as a desktop application.
The desktop application has a number of capabilities that the
Web server does not [desktop mode];
we highly recommend it for frequent BioCyc users.

Definitions of Terminology on the BioCyc Website

Here we define a few key terms. See the glossary for
more definitions.

Pathway/Genome Database (PGDB). A database that describes

The genome of an organism -- its chromosome(s), genes, and genome sequence

The product of each gene

The metabolic network of the organism -- its pathways,
reactions, enzymes, and metabolites

The transporter complement of the organism

The regulatory network of the organism, including its operons,
transcription factors, and the interactions between transcription
factors and their small-molecule ligands and DNA binding sites

Tier 2 PGDB.
PGDBs in Tier 2 were generated by the PathoLogic
program, which predicted their metabolic pathways; their operons (for bacteria only); and
some missing enzymes in their predicted pathways (pathway hole fillers). The resulting PGDBs
underwent manual review by a person to remove false-positive pathway
predictions that they could detect, and to perform
refinements such as defining protein complexes. The resulting PGDBs
also underwent a period of literature-based curation, such as
to enter metabolic pathways that had been experimentally elucidated
in the organism but that were not inferred by PathoLogic. [list of Tier 2 PGDBs]

Pathway Tools Software.Pathway Tools is used to
construct, update, visualize, query, and analyze PGDBs, such as the BioCyc collection.
It is freely available to academics interested in creating PGDBs for
organisms of interest to them.
Components of Pathway Tools are:

The Pathway/Genome
Navigator supports querying, visualization, and analysis of PGDBs

The Pathway/Genome Editors support interactive updating
and refinement of PGDBs